it seems as if there is a bug in the current upload routine. The method CheckWritePermissions in RadFileExplorer.cs does a validation that will always fail for subfolders of a given uploadpath.
In line 905 where it says
|&& uploadFolder[uploadPath.Length] == pathSeparator
it should rather be
|&& uploadFolder[uploadPath.Length -1] == pathSeparator
otherwise this method will always return false when you're uploading into a subfolder of a given uploadpath string.